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Chen C, Zhu T, Liu X, Zhu D, Zhang Y, Wu S, Han C, Zhang H, Luo J, Kong L. Identification of a novel PHGDH covalent inhibitor by chemical proteomics and phenotypic profiling. Acta Pharm Sin B 2022; 12:246-261. [PMID: 35127383 PMCID: PMC8799887 DOI: 10.1016/j.apsb.2021.06.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/03/2021] [Accepted: 05/21/2021] [Indexed: 12/26/2022] Open
Abstract
The first rate-limiting enzyme of the serine synthesis pathway (SSP), phosphoglycerate dehydrogenase (PHGDH), is hyperactive in multiple tumors, which leads to the activation of SSP and promotes tumorigenesis. However, only a few inhibitors of PHGDH have been discovered to date, especially the covalent inhibitors of PHGDH. Here, we identified withangulatin A (WA), a natural small molecule, as a novel covalent inhibitor of PHGDH. Affinity-based protein profiling identified that WA could directly bind to PHGDH and inactivate the enzyme activity of PHGDH. Biolayer interferometry and LC-MS/MS analysis further demonstrated the selective covalent binding of WA to the cysteine 295 residue (Cys295) of PHGDH. With the covalent modification of Cys295, WA blocked the substrate-binding domain (SBD) of PHGDH and exerted an allosteric effect to induce PHGDH inactivation. Further studies revealed that with the inhibition of PHGDH mediated by WA, the glutathione synthesis was decreased and intracellular levels of reactive oxygen species (ROS) were elevated, leading to the inhibition of tumor proliferation. This study indicates WA as a novel PHGDH covalent inhibitor, which identifies Cys295 as a novel allosteric regulatory site of PHGDH and holds great potential in developing anti-tumor agents for targeting PHGDH.
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Key Words
- 3-PG, 3-phosphoglycerate
- 3-PHP, 3-phosphohydroxypyruvate
- ABPP, affinity-based protein profiling
- BLI, biolayer interferometry assay
- CETSA, cellular thermal shift assay
- Chemical proteomics
- Colon cancer
- Covalent inhibitor
- CuAAC, copper-catalyzed alkyne–azide cycloaddition
- DARTS, drug affinity responsive target stability
- GSH, glutathione
- MD, molecular dynamics
- NADPH, nicotinamide adenine dinucleotide phosphate
- Oxidative stress
- PHGDH, phosphoglycerate dehydrogenase
- PSAT, phosphoserine aminotransferase
- Phosphoglycerate dehydrogenase
- RMSD, root mean square deviation
- RMSF, root mean square fluctuations
- ROS, reactive oxygen species
- SBD, substrate-binding domain
- SSP, serine synthesis pathway
- Serine synthesis pathway
- TBTA, tris[(1-benzyl-1H-1,2,3-triazol-4-yl)methyl]amine
- TCEP, tris(2-carboxyethyl) phosphine
- Withangulatin A
- Withanolides
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Affiliation(s)
| | | | | | | | | | | | | | | | - Jianguang Luo
- Corresponding authors. Tel./fax: +86 25 83271405, +86 25 83271402.
| | - Lingyi Kong
- Corresponding authors. Tel./fax: +86 25 83271405, +86 25 83271402.
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Opladen T, Cortès-Saladelafont E, Mastrangelo M, Horvath G, Pons R, Lopez-Laso E, Fernández-Ramos JA, Honzik T, Pearson T, Friedman J, Scholl-Bürgi S, Wassenberg T, Jung-Klawitter S, Kuseyri O, Jeltsch K, Kurian MA, Garcia-Cazorla À. The International Working Group on Neurotransmitter related Disorders (iNTD): A worldwide research project focused on primary and secondary neurotransmitter disorders. Mol Genet Metab Rep 2016; 9:61-66. [PMID: 27830117 PMCID: PMC5094101 DOI: 10.1016/j.ymgmr.2016.09.006] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 09/29/2016] [Indexed: 11/18/2022] Open
Abstract
Introduction Neurotransmitters are chemical messengers that enable communication between the neurons in the synaptic cleft. Inborn errors of neurotransmitter biosynthesis, breakdown and transport are a group of very rare neurometabolic diseases resulting in neurological impairment at any age from newborn to adulthood. Methods and results The International Working Group on Neurotransmitter related Disorders (iNTD) is the first international network focusing on the study of primary and secondary neurotransmitter disorders. It was founded with the aim to foster exchange and improve knowledge in the field of these rare diseases. The newly established iNTD patient registry for neurotransmitter related diseases collects longitudinal data on the natural disease course, approach to diagnosis, therapeutic strategies, and quality of life of affected patients. The registry forms the evidence base for the development of consensus guidelines for patients with neurotransmitter related disorders. Conclusion The iNTD network and registry will improve knowledge and strengthen research capacities in the field of inborn neurotransmitter disorders. The evidence-based guidelines will facilitate standardized diagnostic procedures and treatment approaches.
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Key Words
- 3-PGDH, 3-phosphoglycerat dehydrogenase
- 3-PGH, 3-phosphoglycerat dehydrogenase
- 3-PSP, 3-phosphoserine phosphatase
- 5-MTHF, 5-methyltetrahydrofolate
- AADC, aromatic l-amino acid decarboxylase
- AR/ADGTPCH, autosomal recessive/dominant GTP-cyclohydrolase deficiency
- BH4, tetrahydrobiopterin
- DAT, dopamine transporter
- DHFR, dihydrofolate reductase deficiency
- DHPR, dihydropteridine reductase
- Database
- Dopamine
- DßH, dopamine β-hydroxylase
- FOLR1, folate receptor alpha
- GABA
- GABA, gamma aminobutyric acid
- Glycine
- Guideline
- MAOA, monoamine oxidase A
- NKH, nonketotic hyperglycinemia
- NOS, nitric oxide synthase
- Network
- Neurotransmitter
- PAH, phenylalanine hydroxylase
- PSAT, phosphoserine aminotransferase
- PTPS, 6-pyruvoyl-tetrahydropterin synthase
- Patient registry
- SR, sepiapterin reductase
- SSADH, succinic semialdehyde dehydrogenase
- Serine
- Serotonin
- TH, tyrosine hydroxylase
- TPH, tryptophan hydroxylase
- VMAT, vesicular monoamine transporter
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Affiliation(s)
- Thomas Opladen
- Division of Child Neurology and Metabolic Diseases, University Children's Hospital Heidelberg, Germany
| | | | - Mario Mastrangelo
- Department of Pediatrics and Child Neuropsychiatry, Sapienza Università di Roma, Rome, Italy
| | - Gabriella Horvath
- Division of Biochemical Diseases, BC, Childrens Hospital, Vancouver, Canada
| | - Roser Pons
- First Department of Pediatrics, Pediatric Neurology Unit, Agia Sofia Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Eduardo Lopez-Laso
- Department of Pediatric Neurology, Reina Sofia University Hospital, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), University of Cordoba, CIBERER-ISCIII, Cordoba, Spain
| | - Joaquín A Fernández-Ramos
- Department of Pediatric Neurology, Reina Sofia University Hospital, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), University of Cordoba, CIBERER-ISCIII, Cordoba, Spain
| | - Tomas Honzik
- Dep. of Pediatrics, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Prague, Czech Republic
| | - Toni Pearson
- Department of Neurology, Washington University School of Medicine, St. Louis, USA
| | - Jennifer Friedman
- Department of Neurosciences, University of California San Diego, Division of Neurology Rady Children's Hospital, Rady Children's Institute Genomic Medicine, San Diego, USA
| | - Sabine Scholl-Bürgi
- Department of Pediatrics I, Inherited Metabolic Disorders, Medical University of Innsbruck, Anichstrasse 35, 6020 Innsbruck, Austria
| | - Tessa Wassenberg
- Department of Neurology and Child Neurology, Radboudumc Nijmegen, Donders Institute of Brain Cognition and Behaviour, The Netherlands
| | - Sabine Jung-Klawitter
- Division of Child Neurology and Metabolic Diseases, University Children's Hospital Heidelberg, Germany
| | - Oya Kuseyri
- Division of Child Neurology and Metabolic Diseases, University Children's Hospital Heidelberg, Germany
| | - Kathrin Jeltsch
- Division of Child Neurology and Metabolic Diseases, University Children's Hospital Heidelberg, Germany
| | - Manju A Kurian
- Developmental Neurosciences, UCL- Institute of Child Health and Department of Neurology, Great Ormond Street Hospital for Children NHS Foundations Trust, London, United Kingdom
| | - Àngels Garcia-Cazorla
- Department of Child Neurology, Neurometabolic Unit, CIBERER-ISCIII, Hospital Sant Joan de Déu Barcelona, Spain
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Pinweha P, Rattanapornsompong K, Charoensawan V, Jitrapakdee S. MicroRNAs and oncogenic transcriptional regulatory networks controlling metabolic reprogramming in cancers. Comput Struct Biotechnol J 2016; 14:223-33. [PMID: 27358718 PMCID: PMC4915959 DOI: 10.1016/j.csbj.2016.05.005] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 05/25/2016] [Accepted: 05/27/2016] [Indexed: 12/15/2022] Open
Abstract
Altered cellular metabolism is a fundamental adaptation of cancer during rapid proliferation as a result of growth factor overstimulation. We review different pathways involving metabolic alterations in cancers including aerobic glycolysis, pentose phosphate pathway, de novo fatty acid synthesis, and serine and glycine metabolism. Although oncoproteins, c-MYC, HIF1α and p53 are the major drivers of this metabolic reprogramming, post-transcriptional regulation by microRNAs (miR) also plays an important role in finely adjusting the requirement of the key metabolic enzymes underlying this metabolic reprogramming. We also combine the literature data on the miRNAs that potentially regulate 40 metabolic enzymes responsible for metabolic reprogramming in cancers, with additional miRs from computational prediction. Our analyses show that: (1) a metabolic enzyme is frequently regulated by multiple miRs, (2) confidence scores from prediction algorithms might be useful to help narrow down functional miR-mRNA interaction, which might be worth further experimental validation. By combining known and predicted interactions of oncogenic transcription factors (TFs) (c-MYC, HIF1α and p53), sterol regulatory element binding protein 1 (SREBP1), 40 metabolic enzymes, and regulatory miRs we have established one of the first reference maps for miRs and oncogenic TFs that regulate metabolic reprogramming in cancers. The combined network shows that glycolytic enzymes are linked to miRs via p53, c-MYC, HIF1α, whereas the genes in serine, glycine and one carbon metabolism are regulated via the c-MYC, as well as other regulatory organization that cannot be observed by investigating individual miRs, TFs, and target genes.
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Key Words
- 2-HG, 2-hydroxyglutarate
- ACC, acetyl-CoA carboxylase
- ACL, ATP-citrate lyase
- BRCA1, breast cancer type 1 susceptibility protein
- Cancer
- FAS, fatty acid synthase
- FH, fumarate hydratase
- G6PD, glucose-6-phosphate dehydrogenase
- GDH, glutamate dehydrogenase
- GLS, glutaminase
- GLUT, glucose transporter
- HIF1α, hypoxia inducible factor 1α
- HK, hexokinase
- IDH, isocitrate dehydrogenase
- MCT, monocarboxylic acid transporter
- ME, malic enzyme
- Metabolism
- MicroRNA
- Oncogene
- PC, pyruvate carboxylase
- PDH, pyruvate dehydrogenase
- PDK, pyruvate dehydrogenase kinase
- PEP, phosphoenolpyruvate
- PEPCK, phosphoenolpyruvate carboxykinase
- PFK, phosphofructokinase
- PGK, phosphoglycerate kinase (PGK)
- PHGDH, phosphoglycerate dehydrogenase
- PKM, muscle-pyruvate kinase
- PPP, pentose phosphate pathway
- PSAT, phosphoserine aminotransferase
- PSPH, phosphoserine phosphatase
- SDH, succinate dehydrogenase
- SHMT, serine hydroxymethyl transferase
- SREBP1, sterol regulatory element binding protein 1
- TCA, tricarboxylic acid
- TFs, transcription factors
- Transcriptional regulation network
- c-MYC, V-myc avian myelocytomatosis viral oncogene homolog
- miR/miRNA, LDH, lactate dehydrogenase micro RNA
- p53, tumor protein p53
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Affiliation(s)
- Pannapa Pinweha
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | | | - Varodom Charoensawan
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
- Integrative Computational BioScience (ICBS) Center, Mahidol University, Nakhon Pathom 73170, Thailand
| | - Sarawut Jitrapakdee
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
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